These Paleo Morning Glory Muffins are perfect for breakfast and snacking! Loaded with goodies like apples, carrots, raisins and pecans and flavored with orange zest, these tender and moist muffins absolutely delicious, healthy, gluten free, grain free, dairy free, and refined sugar free.

Morning glory muffins really have the best of everything when it comes to muffins!
Fruit + veggies, warm spices, moist, tender, and healthy!
They’re the best combination of my apple muffins, orange pecan muffins and carrot cake.
Hmmm, does that sound just a little bit strange? Let me tell you – it’s delicious!
The orange zest combined with the raisins and pecans is soooo good.
The apple and carrot make the muffins moist but definitely not TOO moist (as paleo muffins can sometimes be).
Whether you grab one for breakfast or a snack, they’re the perfect grain free bite to satisfy a sweet tooth.

What You Need to Make Paleo Morning Glory Muffins
This recipe is loaded with real-food goodies! Which DOES mean there are a few more ingredients in here than many of my muffin recipes.
But well worth it for the nutrition AND flavor.
Here’s what you’ll need to prepare the muffins:
- blanched almond flour
- flaxseed meal or golden flaxseed meal
- baking soda
- baking powder
- ground cinnamon
- ground ginger
- fine sea salt
- eggs
- maple sugar or coconut sugar
- pure maple syrup or raw honey
- refined coconut oil
- unsweetened applesauce
- orange zest
- fresh orange juice
- pure vanilla extract
- grated carrots
- grated apple
- raisins
- pecans

How to Make Paleo Morning Glory Muffins
Preheat your oven to 350° F and line 2 muffins pans with 15 parchment liners. In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon and salt, set aside.
In a separate mixing bowl, whisk together the eggs, sugar, syrup or honey, coconut oil, applesauce, orange zest and juice and vanilla until smooth.
Fold in the grated carrots and apples (after squeezing out as much water as possible) then gently stir the dry ingredients into the wet until no flour spots show.
Fold in the raisins and pecans, then fill the muffin liners just above the top, (batter will be thick). You will make 14-15 muffins.
Bake for 23-28 minutes, until golden brown on top and set in the center. A toothpick inserted near the center of a muffin should come out with a few crumbs.
Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins from the pan (in their liners) and continue to cool to room temperature.
Store muffins at room temperature for the first day (loosely covered) then in the refrigerator for up to 5 days. Enjoy!

Tips for the Perfect Paleo Morning Glory Muffins
Paleo baked goods can get soggy – yes, it’s true! Especially when baking with fruits and veggies.
Because the flours used are high in fat and can be dense, even a little bit of extra water from ingredients can weigh the muffins down and create a less than ideal level of moistness – ugh – not my favorite!
Since you have carrots, apples and applesauce in this recipe you need to be extra careful about removing excess moisture from the apples and carrots.
Don’t just drain on paper towels, make sure you squeeze out as much water as possible before adding to the batter.
Grain Free Baking Powder
Now, for baking powder! I am okay to use an aluminum free baking powder, which is not technically paleo due to the corn starch.
If you want to make your own grain free and paleo version, it’s actually really easy.
Simply mix 1 tsp baking soda with 2 tsp cream of tartar.
For this recipe, you will need just 1 tsp total of this mixture.

Storing Paleo Morning Glory Muffins
I kept my muffins out on the countertop, loosely covered, for the first day and they were perfect. After that, I placed them in a sealed container and kept them in the refrigerator for the next few days.
They should last up to 5 days in the refrigerator. I like to pop them in the toaster oven to warm them up a little after they’ve been refrigerated.
They’re so good with a little extra ghee or grass-fed butter and honey!
I hope you’re ready for a delicious addition to your mornings with these paleo morning glory muffins! Grab your ingredients and preheat your oven – it’s time to bake!
Paleo Morning Glory Muffins {Gluten Free, Dairy Free}

Paleo Morning Glory Muffins {Gluten-Free, Dairy-Free}

Ingredients
- 2 1/2 cups blanched almond flour
- 1/2 cup flaxseed meal or golden flaxseed meal
- 1 tsp baking soda
- 1 tsp aluminum free baking powder
- 1 Tbsp ground cinnamon
- 1/2 tsp fine sea salt
- 3 large eggs
- 1/2 cup coconut sugar or maple sugar
- 1/4 cup pure maple syrup or raw honey
- 1/4 cup melted refined coconut oil
- 1/4 cup unsweetened applesauce
- 1 tsp orange zest
- 2 Tbsp orange juice
- 2 tsp pure vanilla extract
- 1 cup grated carrots about 2 large
- 1 cup grated apple about 1 large, squeezed with paper towels to remove excess water
- 1/2 cup raisins
- 1/2 cup chopped pecans
Instructions
-
Preheat your oven to 350° F and line 2 muffins pans with 15 parchment liners.
-
In a large bowl, mix together the almond flour, flaxseed meal, baking soda, baking powder, cinnamon and salt, set aside.
-
In a separate mixing bowl, whisk together the eggs, sugar, syrup or honey, coconut oil, applesauce, orange zest and juice and vanilla until smooth. Fold in the grated carrots and apples (after squeezing out as much water as possible) then gently stir the dry ingredients into the wet until no flour spots show.
-
Fold in the raisins and pecans, then fill the muffin liners just above the top, (batter will be thick). You will make 14-15 muffins. Bake for 23-28 minutes, until golden brown on top and set in the center. A toothpick inserted near the center of a muffin should come out with a few crumbs.
-
Allow the muffin pan to cool on a wire rack for 10 minutes, then carefully remove the muffins from the pan (in their liners) and continue to cool to room temperature. Store muffins at room temperature for the first day (loosely covered) then in the refrigerator for up to 5 days. Enjoy!
Nutrition
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Want More Paleo Muffin Recipes? Try One of These!
Cranberry Orange Pecan Muffins
Blueberry Muffins with Almond Streusel
Cinnamon Raisin Sweet Potato Muffins
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Loved this! So delish! Wasn’t sure how the Orange would be but turned out great.
Love the combo of orange zest grated apple and grated carrot! Tastes great but has trouble holding together. They get messy and crumbly quick. Refrigerating does help. Thanks for sharing/creating! One of my sons is grain free and I love finding baked goods I can feed him. Scaled way back on maple syrup and only added half of recommended coconut sugar. I subbed walnut, butter and coconut flour for the pecans, coconut oil and flaxseed meal and all turned out just fine. Anyone try to do this completely vegan?
Does anyone have any substitution suggestions for the apple sauce?
I used banana instead!
Just ate one warm from the oven because I couldn’t wait. 🙂 Delicious flavor! I made a half batch and used two eggs, went the maple syrup route, and had to used cane sugar because I didn’t have another option. They didn’t rise as much as I hoped, but they’re not stodgy in texture like a lot of gluten-free cakes. My favorite part is the crusty top, so next time I may try baking in a pan to get more surface area, and also will give it a little more time. (I stopped at 25 minutes.) Thanks for the recipe!! <3
These muffins look so tasty. Amazing, I will surely gonna try it out.
Very tasty! & healthy ingredients
Absolutely delicious!!!
Only thing I changed was changed the coconut sugar to monk fruit ( cut the amount in half)
Will definitely be making again
Yummy
These are the best muffins I’ve ever had! So good!
Very good!! Gonna even put less honey in next time (I added chopped dates for sweetness) and more nuts…yummy!